build(deps-dev): bump ihm from 0.36 to 2.2

[dependabot]

Bumps ihm from 0.36 to 2.2.

Release notes

Sourced from ihm's releases.

python-ihm 2.2 release

• The C-accelerated BinaryCIF parser now supports a wider range of data types.

Full Changelog: ihmwg/python-ihm@2.1...2.2

python-ihm 2.1 release

• Minor fixes to the C-accelerated BinaryCIF parser.

Full Changelog: ihmwg/python-ihm@2.0...2.1

python-ihm 2.0 release

• python-ihm no longer supports Python 2; the oldest supported version is now Python 3.6 (#161).
• BinaryCIF files are now read in using a C-accelerated parser, which is faster and more memory efficient than the older Python parser (#160).
• The tokenizers for mmCIF and BinaryCIF now return data of the correct type (int, float, bool, or string); previously, all values were returned as strings. ihm.reader.Handler subclasses now request data of the correct type using Python type annotations. The API of the C-accelerated parsers has changed accordingly (#162).
• The new ihm.metadata.BinaryCIFParser class can extract metadata such as database IDs and template information from BinaryCIF files, in a similar fashion to the existing ihm.metadata.CIFParser.
• Information about a deposited structure, such as the deposition date, can now be read from System.database_status (#163).
• The new ihm.format.ReplaceCategoryFilter class can be used to completely replace or remove an mmCIF category when using ihm.format.CifTokenReader.

Full Changelog: ihmwg/python-ihm@1.8...2.0

python-ihm 1.8 release

• Support added for datasets containing EPR, X-ray diffraction, footprinting or predicted contacts using the ihm.dataset.EPRDataset, ihm.dataset.XRayDiffractionDataset, ihm.dataset.HydroxylRadicalFootprintingDataset, ihm.dataset.DNAFootprintingDataset and ihm.dataset.PredictedContactsDataset classes (#157).
• Revision information (in the pdbx_audit_revision_* mmCIF tables) can now be read or written using the new ihm.Revision and ihm.RevisionDetails classes (#156).
• The new ihm.location.BMRbigLocation class allows for referencing datasets stored in the BMRbig database.
• All references to the old PDB-Dev database are now updated to PDB-IHM.

Full Changelog: ihmwg/python-ihm@1.7...1.8

python-ihm 1.7 release

• Sanity checks when writing out a file can now be disabled if desired, using the new check argument to ihm.dumper.write (#153).
• Data that have been split over multiple mmCIF or BinaryCIF files can now be combined into a single ihm.System object using the new add_to_system argument to ihm.reader.read.
• Input files that assign multiple ihm.location.Location objects to a single ihm.dataset.Dataset can now be read (#151).
• Bugfix: multiple ihm.restraint.EM3DRestraint and ihm.restraint.SASRestraint objects can now be created for a single dataset, as long as they act on different assemblies, as allowed by the dictionary.
• Bugfix: allow for non-standard residues in the struct_ref table (#154).

Full Changelog: ihmwg/python-ihm@1.6...1.7

python-ihm 1.6 release

• The new class ihm.model.NotModeledResidueRange allows for the annotation of residue ranges that were explicitly not modeled. These are written to the _ihm_residues_not_modeled mmCIF table, and any residue marked as not-modeled in all models will also be excluded from the pdbx_poly_seq_scheme table.
• The make_mmcif utility script will now automatically add any missing ihm.model.NotModeledResidueRange objects for not-modeled residue ranges (#150).
• Bugfix: the residue range checks introduced in version 1.5 broke the API used by python-modelcif. They have been reimplemented using the original API.
• Bugfix: an unknown (?) value for pdbx_poly_seq_scheme.auth_seq_num is now preserved, not silently removed, when reading an mmCIF file.

Full Changelog: ihmwg/python-ihm@1.5...1.6

python-ihm 1.5 release

• Trying to create a ihm.Residue, ihm.EntityRange, or ihm.AsymUnitRange that references out-of-range residues (i.e. seq_id less than 1 or beyond the length of the ihm.Entity sequence) will now raise an error.
• Bugfix: ihm.reference.Reference objects are no longer given erroneous duplicate IDs on output (#149).

... (truncated)

Changelog

Sourced from ihm's changelog.

2.2 - 2025-02-13

• The C-accelerated BinaryCIF parser now supports a wider range of data types.

2.1 - 2025-02-12

• Minor fixes to the C-accelerated BinaryCIF parser.

2.0 - 2025-02-11

• python-ihm no longer supports Python 2; the oldest supported version is now Python 3.6 (#161).
• BinaryCIF files are now read in using a C-accelerated parser, which is faster and more memory efficient than the older Python parser (#160).
• The tokenizers for mmCIF and BinaryCIF now return data of the correct type (int, float, bool, or string); previously, all values were returned as strings. :class:ihm.reader.Handler subclasses now request data of the correct type using Python type annotations. The API of the C-accelerated parsers has changed accordingly (#162).
• The new :class:ihm.metadata.BinaryCIFParser class can extract metadata such as database IDs and template information from BinaryCIF files, in a similar fashion to the existing :class:ihm.metadata.CIFParser.
• Information about a deposited structure, such as the deposition date, can now be read from :attr:System.database_status (#163).
• The new :class:ihm.format.ReplaceCategoryFilter class can be used to completely replace or remove an mmCIF category when using :class:ihm.format.CifTokenReader.

1.8 - 2024-11-26

• Support added for datasets containing EPR, X-ray diffraction, footprinting or predicted contacts using the :class:ihm.dataset.EPRDataset, :class:ihm.dataset.XRayDiffractionDataset, :class:ihm.dataset.HydroxylRadicalFootprintingDataset, :class:ihm.dataset.DNAFootprintingDataset and :class:ihm.dataset.PredictedContactsDataset classes (#157).
• Revision information (in the pdbx_audit_revision_* mmCIF tables) can now be read or written using the new :class:ihm.Revision and :class:ihm.RevisionDetails classes (#156).
• The new :class:ihm.location.BMRbigLocation class allows for referencing datasets stored in the BMRbig database.
• All references to the old PDB-Dev database are now updated to PDB-IHM.

1.7 - 2024-10-22

• Sanity checks when writing out a file can now be disabled if desired, using the new check argument to :func:ihm.dumper.write (#153).
• Data that have been split over multiple mmCIF or BinaryCIF files can now be combined into a single :class:ihm.System object using the new add_to_system argument to :func:ihm.reader.read.

... (truncated)

Commits

• d49b379 Update for 2.2 release
• 545ffbe Add support for 16-bit int BinaryCIF column data
• e4a7b50 Add support for signed 8-bit BinaryCIF column data
• 48f30be Update for 2.1 release
• 10c124b Also test with BinaryCIF if we can
• 9f9bc1e Test self-test scripts in each package
• 206d964 Support 32-bit float column data
• bca8d4f Map out of range StringArray indices to empty strings
• 496b0f7 Fix typo
• caba7ee Update for 2.0 release
• Additional commits viewable in compare view

Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting @dependabot rebase.

---

Dependabot commands and options

You can trigger Dependabot actions by commenting on this PR:

• @dependabot rebase will rebase this PR
• @dependabot recreate will recreate this PR, overwriting any edits that have been made to it
• @dependabot merge will merge this PR after your CI passes on it
• @dependabot squash and merge will squash and merge this PR after your CI passes on it
• @dependabot cancel merge will cancel a previously requested merge and block automerging
• @dependabot reopen will reopen this PR if it is closed
• @dependabot close will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually
• @dependabot show <dependency name> ignore conditions will show all of the ignore conditions of the specified dependency
• @dependabot ignore this major version will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)
• @dependabot ignore this minor version will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)
• @dependabot ignore this dependency will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)